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Numaguchi Y, Tsukakoshi K, Takeuchi N, Suzuki Y, Ikebukuro K, Kawano R. Real-time monitoring of the amyloid β 1-42 monomer-to-oligomer channel transition using a lipid bilayer system. PNAS NEXUS 2024; 3:pgad437. [PMID: 38156289 PMCID: PMC10753159 DOI: 10.1093/pnasnexus/pgad437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 12/06/2023] [Indexed: 12/30/2023]
Abstract
This study describes the observation of the transformation of monomeric amyloid β1-42 (Aβ42) into oligomers in a lipid membrane utilizing a lipid bilayer system for electrophysiological measurement. The relevance of oligomers and protofibrils in Alzheimer's disease (AD) is underscored given their significant neurotoxicity. By closely monitoring the shift of Aβ42 from its monomeric state to forming oligomeric channels in phospholipid membranes, we noted that this transformation transpired within a 2-h frame. We manipulated the lipid membrane's constitution with components such as glycerophospholipid, porcine brain total lipid extract, sphingomyelin (SM), and cholesterol (Chol.) to effectively imitate nerve cell membranes. Interesting findings showcased Chol.'s ability to foster stable oligomeric channel formation in the lipid membrane, with SM and GM1 lipids potentially enhancing channel formation as well. Additionally, the study identified the potential of a catechin derivative, epigallocatechin gallate (EGCG), in obstructing oligomerization. With EGCG present in the outer solution of the Aβ42-infused membrane, a noteworthy reduction in channel current was observed, suggesting the successful inhibition of oligomerization. This conclusion held true in both, prior and subsequent, stages of oligomerization. Our findings shed light on the toxicity of oligomers, promising invaluable information for future advancements in AD treatment strategies.
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Affiliation(s)
- Yuri Numaguchi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo 184-0011, Japan
| | - Kaori Tsukakoshi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo 184-0011, Japan
| | - Nanami Takeuchi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo 184-0011, Japan
| | - Yuki Suzuki
- Department of Chemistry for Materials, Graduate School of Engineering, Mie University, Mie 514-0102, Japan
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo 184-0011, Japan
| | - Ryuji Kawano
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo 184-0011, Japan
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2
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Yang Y, Distaffen H, Jalali S, Nieuwkoop AJ, Nilsson BL, Dias CL. Atomic Insights into Amyloid-Induced Membrane Damage. ACS Chem Neurosci 2022; 13:2766-2777. [PMID: 36095304 DOI: 10.1021/acschemneuro.2c00446] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Amphipathic peptides can cause biological membranes to leak either by dissolving their lipid content via a detergent-like mechanism or by forming pores on the membrane surface. These modes of membrane damage have been related to the toxicity of amyloid peptides and to the activity of antimicrobial peptides. Here, we perform the first all-atom simulations in which membrane-bound amphipathic peptides self-assemble into β-sheets that subsequently either form stable pores inside the bilayer or drag lipids out of the membrane surface. An analysis of these simulations shows that the acyl tail of lipids interact strongly with non-polar side chains of peptides deposited on the membrane. These strong interactions enable lipids to be dragged out of the bilayer by oligomeric structures accounting for detergent-like damage. They also disturb the orientation of lipid tails in the vicinity of peptides. These distortions are minimized around pore structures. We also show that membrane-bound β-sheets become twisted with one of their extremities partially penetrating the lipid bilayer. This allows peptides on opposite leaflets to interact and form a long transmembrane β-sheet, which initiates poration. In simulations, where peptides are deposited on a single leaflet, the twist in β-sheets allows them to penetrate the membrane and form pores. In addition, our simulations show that fibril-like structures produce little damage to lipid membranes, as non-polar side chains in these structures are unavailable to interact with the acyl tail of lipids.
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Affiliation(s)
- Yanxing Yang
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
| | - Hannah Distaffen
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Sharareh Jalali
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
| | - Andrew J Nieuwkoop
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Bradley L Nilsson
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Cristiano L Dias
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
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3
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Kim M, Son J, Kim Y. NMR Studies of the Ion Channel-Forming Human Amyloid-β with Zinc Ion Concentrations. MEMBRANES 2021; 11:membranes11110799. [PMID: 34832029 PMCID: PMC8620595 DOI: 10.3390/membranes11110799] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 10/06/2021] [Accepted: 10/14/2021] [Indexed: 11/16/2022]
Abstract
Alzheimer’s disease (AD) is classified as an amyloid-related disease. Amyloid beta (Aβ) is a transmembrane protein known to play a major role in the pathogenesis of AD. These Aβ proteins can form ion channels or pores in the cell membrane. Studies have elucidated the structure of the transmembrane domain of Aβ ion channels. In addition, various studies have investigated substances that block or inhibit the formation of Aβ ion channels. Zinc ions are considered as potential inhibitors of AD. In this study, we focused on the transmembrane domain and some external domains of the Aβ protein (hAPP-TM), and solution-state NMR was used to confirm the effect on residues of the protein in the presence of zinc ions. In addition, we sought to confirm the structure and orientation of the protein in the presence of the bicelle using solid-state NMR.
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Affiliation(s)
| | | | - Yongae Kim
- Correspondence: ; Tel.: +82-31-330-4604; Fax: +82-31-330-4566
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4
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Smirnov MA, Tolmachev DA, Glova AD, Sokolova MP, Geydt PV, Lukasheva NV, Lyulin SV. Combined Use of Atomic Force Microscopy and Molecular Dynamics in the Study of Biopolymer Systems. POLYMER SCIENCE SERIES C 2021. [DOI: 10.1134/s1811238221020089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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5
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Gomes GN, Levine ZA. Defining the Neuropathological Aggresome across in Silico, in Vitro, and ex Vivo Experiments. J Phys Chem B 2021; 125:1974-1996. [PMID: 33464098 PMCID: PMC8362740 DOI: 10.1021/acs.jpcb.0c09193] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The loss of proteostasis over the life course is associated with a wide range of debilitating degenerative diseases and is a central hallmark of human aging. When left unchecked, proteins that are intrinsically disordered can pathologically aggregate into highly ordered fibrils, plaques, and tangles (termed amyloids), which are associated with countless disorders such as Alzheimer's disease, Parkinson's disease, type II diabetes, cancer, and even certain viral infections. However, despite significant advances in protein folding and solution biophysics techniques, determining the molecular cause of these conditions in humans has remained elusive. This has been due, in part, to recent discoveries showing that soluble protein oligomers, not insoluble fibrils or plaques, drive the majority of pathological processes. This has subsequently led researchers to focus instead on heterogeneous and often promiscuous protein oligomers. Unfortunately, significant gaps remain in how to prepare, model, experimentally corroborate, and extract amyloid oligomers relevant to human disease in a systematic manner. This Review will report on each of these techniques and their successes and shortcomings in an attempt to standardize comparisons between protein oligomers across disciplines, especially in the context of neurodegeneration. By standardizing multiple techniques and identifying their common overlap, a clearer picture of the soluble neuropathological aggresome can be constructed and used as a baseline for studying human disease and aging.
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Affiliation(s)
- Gregory-Neal Gomes
- Department of Pathology, Yale School of Medicine, New Haven, CT, 06520, USA
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Zachary A. Levine
- Department of Pathology, Yale School of Medicine, New Haven, CT, 06520, USA
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA
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6
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Yang J, Agnihotri MV, Huseby CJ, Kuret J, Singer SJ. A theoretical study of polymorphism in VQIVYK fibrils. Biophys J 2021; 120:1396-1416. [PMID: 33571490 DOI: 10.1016/j.bpj.2021.01.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 01/07/2021] [Accepted: 01/11/2021] [Indexed: 02/06/2023] Open
Abstract
The VQIVYK fragment from the Tau protein, also known as PHF6, is essential for aggregation of Tau into neurofibrillary lesions associated with neurodegenerative diseases. VQIVYK itself forms amyloid fibrils composed of paired β-sheets. Therefore, the full Tau protein and VQIVYK fibrils have been intensively investigated. A central issue in these studies is polymorphism, the ability of a protein to fold into more than one structure. Using all-atom molecular simulations, we generate five stable polymorphs of VQIVYK fibrils, establish their relative free energy with umbrella sampling methods, and identify the side chain interactions that provide stability. The two most stable polymorphs, which have nearly equal free energy, are formed by interdigitation of the mostly hydrophobic VIY "face" sides of the β-sheets. Another stable polymorph is formed by interdigitation of the QVK "back" sides. When we turn to examine structures from cryo-electron microscopy experiments on Tau filaments taken from diseased patients or generated in vitro, we find that the pattern of side chain interactions found in the two most stable face-to-face as well as the back-to-back polymorphs are recapitulated in amyloid structures of the full protein. Thus, our studies suggest that the interactions stabilizing PHF6 fibrils explain the amyloidogenicity of the VQIVYK motif within the full Tau protein and provide justification for the use of VQIVYK fibrils as a test bed for the design of molecules that identify or inhibit amyloid structures.
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Affiliation(s)
- Jaehoon Yang
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio
| | - Mithila V Agnihotri
- Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, Ohio
| | - Carol J Huseby
- Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, Ohio
| | - Jeff Kuret
- Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, Ohio; Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, Ohio.
| | - Sherwin J Singer
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio; Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, Ohio.
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7
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Li Y, Tang H, Andrikopoulos N, Javed I, Cecchetto L, Nandakumar A, Kakinen A, Davis TP, Ding F, Ke PC. The membrane axis of Alzheimer's nanomedicine. ADVANCED NANOBIOMED RESEARCH 2021; 1:2000040. [PMID: 33748816 PMCID: PMC7971452 DOI: 10.1002/anbr.202000040] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Alzheimer's disease (AD) is a major neurological disorder impairing its carrier's cognitive function, memory and lifespan. While the development of AD nanomedicine is still nascent, the field is evolving into a new scientific frontier driven by the diverse physicochemical properties and theranostic potential of nanomaterials and nanocomposites. Characteristic to the AD pathology is the deposition of amyloid plaques and tangles of amyloid beta (Aβ) and tau, whose aggregation kinetics may be curbed by nanoparticle inhibitors via sequence-specific targeting or nonspecific interactions with the amyloidogenic proteins. As literature implicates cell membrane as a culprit in AD pathogenesis, here we summarize the membrane axis of AD nanomedicine and present a new rationale that the field development may greatly benefit from harnessing our existing knowledge of Aβ-membrane interaction, nanoparticle-membrane interaction and Aβ-nanoparticle interaction.
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Affiliation(s)
- Yuhuan Li
- Zhongshan Hospital, Fudan University, 111 Yixueyuan Rd, Xuhui District, Shanghai, 200032, China
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Huayuan Tang
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
| | - Nicholas Andrikopoulos
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Ibrahim Javed
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Qld 4072, Australia
| | - Luca Cecchetto
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- Department of Chemical and Pharmaceutical Science, University of Trieste, Via Licio Giorgieri 1, 34127 Trieste, Italy
| | - Aparna Nandakumar
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Aleksandr Kakinen
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Qld 4072, Australia
| | - Thomas P. Davis
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Qld 4072, Australia
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
| | - Pu Chun Ke
- Zhongshan Hospital, Fudan University, 111 Yixueyuan Rd, Xuhui District, Shanghai, 200032, China
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
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8
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Panda PK, Grigoriev A, Mishra YK, Ahuja R. Progress in supercapacitors: roles of two dimensional nanotubular materials. NANOSCALE ADVANCES 2020; 2:70-108. [PMID: 36133979 PMCID: PMC9419609 DOI: 10.1039/c9na00307j] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 10/28/2019] [Indexed: 05/03/2023]
Abstract
Overcoming the global energy crisis due to vast economic expansion with the advent of human reliance on energy-consuming labor-saving devices necessitates the demand for next-generation technologies in the form of cleaner energy storage devices. The technology accelerates with the pace of developing energy storage devices to meet the requirements wherever an unanticipated burst of power is indeed needed in a very short time. Supercapacitors are predicted to be future power vehicles because they promise faster charging times and do not rely on rare elements such as lithium. At the same time, they are key nanoscale device elements for high-frequency noise filtering with the capability of storing and releasing energy by electrostatic interactions between the ions in the electrolyte and the charge accumulated at the active electrode during the charge/discharge process. There have been several developments to increase the functionality of electrodes or finding a new electrolyte for higher energy density, but this field is still open to witness the developments in reliable materials-based energy technologies. Nanoscale materials have emerged as promising candidates for the electrode choice, especially in 2D sheet and folded tubular network forms. Due to their unique hierarchical architecture, excellent electrical and mechanical properties, and high specific surface area, nanotubular networks have been widely investigated as efficient electrode materials in supercapacitors, while maintaining their inherent characteristics of high power and long cycling life. In this review, we briefly present the evolution, classification, functionality, and application of supercapacitors from the viewpoint of nanostructured materials to apprehend the mechanism and construction of advanced supercapacitors for next-generation storage devices.
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Affiliation(s)
- Pritam Kumar Panda
- Department of Physics and Astronomy, Uppsala University Box 516 SE-75120 Uppsala Sweden
| | - Anton Grigoriev
- Department of Physics and Astronomy, Uppsala University Box 516 SE-75120 Uppsala Sweden
| | - Yogendra Kumar Mishra
- Mads Clausen Institute, NanoSYD, University of Southern Denmark Alsion 2 DK-6400 Denmark
| | - Rajeev Ahuja
- Department of Materials and Engineering, Royal Institute of Technology (KTH) SE-10044 Stockholm Sweden
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9
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Martinez Hernandez A, Urbanke H, Gillman AL, Lee J, Ryazanov S, Agbemenyah HY, Benito E, Jain G, Kaurani L, Grigorian G, Leonov A, Rezaei-Ghaleh N, Wilken P, Arce FT, Wagner J, Fuhrmann M, Caruana M, Camilleri A, Vassallo N, Zweckstetter M, Benz R, Giese A, Schneider A, Korte M, Lal R, Griesinger C, Eichele G, Fischer A. The diphenylpyrazole compound anle138b blocks Aβ channels and rescues disease phenotypes in a mouse model for amyloid pathology. EMBO Mol Med 2019; 10:32-47. [PMID: 29208638 PMCID: PMC5760857 DOI: 10.15252/emmm.201707825] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Alzheimer's disease is a devastating neurodegenerative disease eventually leading to dementia. An effective treatment does not yet exist. Here we show that oral application of the compound anle138b restores hippocampal synaptic and transcriptional plasticity as well as spatial memory in a mouse model for Alzheimer's disease, when given orally before or after the onset of pathology. At the mechanistic level, we provide evidence that anle138b blocks the activity of conducting Aβ pores without changing the membrane embedded Aβ-oligomer structure. In conclusion, our data suggest that anle138b is a novel and promising compound to treat AD-related pathology that should be investigated further.
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Affiliation(s)
- Ana Martinez Hernandez
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany.,Department for Genes and Behavior, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Hendrik Urbanke
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Alan L Gillman
- Department of Bioengineering, Materials Science and Engineering, Department of Mechanical and Aerospace Engineering and Institute of Engineering in Medicine, University of California San Diego, La Jolla, CA, USA
| | - Joon Lee
- Department of Bioengineering, Materials Science and Engineering, Department of Mechanical and Aerospace Engineering and Institute of Engineering in Medicine, University of California San Diego, La Jolla, CA, USA
| | - Sergey Ryazanov
- Department of NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,DFG Research Center Nanoscale Microscopy and Molecular Physiology of the Brain, Göttingen, Germany
| | - Hope Y Agbemenyah
- Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, Göttingen, Germany
| | - Eva Benito
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Gaurav Jain
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Lalit Kaurani
- DFG Research Center Nanoscale Microscopy and Molecular Physiology of the Brain, Göttingen, Germany
| | - Gayane Grigorian
- Department of Cellular Neurobiology, Technical University Braunschweig, Braunschweig, Germany
| | - Andrei Leonov
- Department of NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,DFG Research Center Nanoscale Microscopy and Molecular Physiology of the Brain, Göttingen, Germany
| | - Nasrollah Rezaei-Ghaleh
- Department of NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Department of Translational Structural Biology of Dementia, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Petra Wilken
- DFG Research Center Nanoscale Microscopy and Molecular Physiology of the Brain, Göttingen, Germany.,Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, Göttingen, Germany.,Group for Translational Research in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE) Göttingen, Göttingen, Germany
| | - Fernando Teran Arce
- Department of Bioengineering, Materials Science and Engineering, Department of Mechanical and Aerospace Engineering and Institute of Engineering in Medicine, University of California San Diego, La Jolla, CA, USA
| | - Jens Wagner
- Group for Neuroimmunology and Imaging, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Martin Fuhrmann
- Group for Neuroimmunology and Imaging, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Mario Caruana
- Department of Physiology and Biochemistry, Centre for Molecular Medicine and Biobanking, University of Malta, Msida, Malta
| | - Angelique Camilleri
- Department of Physiology and Biochemistry, Centre for Molecular Medicine and Biobanking, University of Malta, Msida, Malta
| | - Neville Vassallo
- Department of Physiology and Biochemistry, Centre for Molecular Medicine and Biobanking, University of Malta, Msida, Malta
| | - Markus Zweckstetter
- Department of NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,DFG Research Center Nanoscale Microscopy and Molecular Physiology of the Brain, Göttingen, Germany.,Department of Translational Structural Biology of Dementia, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany.,Department of Neurology, University Medical Center Göttingen, University of Göttingen, Göttingen, Germany
| | - Roland Benz
- Life Sciences and Chemistry, Jacobs University of Bremen, Bremen, Germany
| | - Armin Giese
- Center for Neuropathology and Prion Research, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Anja Schneider
- DFG Research Center Nanoscale Microscopy and Molecular Physiology of the Brain, Göttingen, Germany.,Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, Göttingen, Germany.,Group for Translational Research in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE) Göttingen, Göttingen, Germany
| | - Martin Korte
- Department of Cellular Neurobiology, Technical University Braunschweig, Braunschweig, Germany .,Helmholtz Center for Infections Research, Braunschweig, Germany
| | - Ratnesh Lal
- Department of Bioengineering, Materials Science and Engineering, Department of Mechanical and Aerospace Engineering and Institute of Engineering in Medicine, University of California San Diego, La Jolla, CA, USA
| | - Christian Griesinger
- Department of NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany .,DFG Research Center Nanoscale Microscopy and Molecular Physiology of the Brain, Göttingen, Germany
| | - Gregor Eichele
- Department for Genes and Behavior, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Andre Fischer
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany .,Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, Göttingen, Germany
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10
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Cheng Q, Hu ZW, Doherty KE, Tobin-Miyaji YJ, Qiang W. The on-fibrillation-pathway membrane content leakage and off-fibrillation-pathway lipid mixing induced by 40-residue β-amyloid peptides in biologically relevant model liposomes. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2018; 1860:1670-1680. [PMID: 29548698 PMCID: PMC6295276 DOI: 10.1016/j.bbamem.2018.03.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 03/08/2018] [Accepted: 03/10/2018] [Indexed: 02/06/2023]
Abstract
Disruption of the synaptic plasma membrane (SPM) induced by the aggregation of β-amyloid (Aβ) peptides has been considered as a potential mechanism for the neurotoxicity of Aβ in Alzheimer's disease (AD). However, the molecular basis of such membrane disruption process remains unclear, mainly because of the severe systematic heterogeneity problem that prevents the high-resolution studies. Our previous studies using a two-component phosphatidylcholine (PC)/phosphatidylglycerol (PG) model liposome showed the presence of Aβ-induced membrane disruptions that were either on the pathway or off the pathway of fibril formation. The present study focuses on a more biologically relevant model membrane with compositions that mimic the outer leaflet of SPMs. The main findings are: (1) the two competing membrane disruption effects discovered in PC/PG liposomes and their general peptide-to-lipid-molar-ratio dependence persist in the more complicated membrane models; (2) the SPM-mimic membrane promotes the formation of certain "on-fibrillation-pathway" intermediates with higher α-helical structural population, which lead to more rapid and significant of membrane content leakage; (3) although the "on-fibrillation-pathway" intermediate structures show dependence on membrane compositions, there seems to be a common final fibril structure grown from different liposomes, suggesting that there may be a predominant fibril structure for 40-residue Aβ (i.e. Aβ40) peptides in biologically-relevant membranes. This article is part of a Special Issue entitled: Protein Aggregation and Misfolding at the Cell Membrane Interface edited by Ayyalusamy Ramamoorthy.
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Affiliation(s)
- Qinghui Cheng
- Department of Chemistry, State University of New York at Binghamton, Binghamton, NY 13902, United States
| | - Zhi-Wen Hu
- Department of Chemistry, State University of New York at Binghamton, Binghamton, NY 13902, United States
| | - Katelynne E Doherty
- Department of Chemistry, State University of New York at Binghamton, Binghamton, NY 13902, United States
| | - Yuto J Tobin-Miyaji
- Department of Chemistry, State University of New York at Binghamton, Binghamton, NY 13902, United States
| | - Wei Qiang
- Department of Chemistry, State University of New York at Binghamton, Binghamton, NY 13902, United States.
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11
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Press-Sandler O, Miller Y. Molecular mechanisms of membrane-associated amyloid aggregation: Computational perspective and challenges. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:1889-1905. [DOI: 10.1016/j.bbamem.2018.03.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 03/07/2018] [Accepted: 03/12/2018] [Indexed: 01/02/2023]
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12
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Liu Y, Ren B, Zhang Y, Sun Y, Chang Y, Liang G, Xu L, Zheng J. Molecular simulation aspects of amyloid peptides at membrane interface. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:1906-1916. [PMID: 29421626 DOI: 10.1016/j.bbamem.2018.02.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 01/31/2018] [Accepted: 02/01/2018] [Indexed: 12/13/2022]
Abstract
The interactions of amyloid peptides with cell membranes play an important role in maintaining the integrity and functionality of cell membrane. A thorough molecular-level understanding of the structure, dynamics, and interactions between amyloid peptides and cell membranes is critical to amyloid aggregation and toxicity mechanisms for the bench-to-bedside applications. Here we review the most recent computational studies of amyloid peptides at model cell membranes. Different mechanisms of action of amyloid peptides on/in cell membranes, targeted by different computational techniques at different lengthscales and timescales, are rationally discussed. Finally, we have proposed some new insights into the remaining challenges and perspectives for future studies to improve our understanding of the activity of amyloid peptides associated with protein-misfolding diseases. This article is part of a Special Issue entitled: Protein Aggregation and Misfolding at the Cell Membrane Interface edited by Ayyalusamy Ramamoorthy.
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Affiliation(s)
- Yonglan Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, College of Life Science and Chemistry, Hunan University of Technology, Zhuzhou 412007, PR China; Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, OH 44325, United States
| | - Baiping Ren
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, OH 44325, United States
| | - Yanxian Zhang
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, OH 44325, United States
| | - Yan Sun
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Yung Chang
- R&D Center for Membrane Technology and Department of Chemical EngineeringChung Yuan Christian University, Chung-Li, Taoyuan 320, Taiwan
| | - Guizhao Liang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, PR China
| | - Lijian Xu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, College of Life Science and Chemistry, Hunan University of Technology, Zhuzhou 412007, PR China; Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, OH 44325, United States.
| | - Jie Zheng
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, OH 44325, United States.
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13
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Coskuner-Weber O, Uversky VN. Insights into the Molecular Mechanisms of Alzheimer's and Parkinson's Diseases with Molecular Simulations: Understanding the Roles of Artificial and Pathological Missense Mutations in Intrinsically Disordered Proteins Related to Pathology. Int J Mol Sci 2018; 19:E336. [PMID: 29364151 PMCID: PMC5855558 DOI: 10.3390/ijms19020336] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Revised: 01/14/2018] [Accepted: 01/16/2018] [Indexed: 12/18/2022] Open
Abstract
Amyloid-β and α-synuclein are intrinsically disordered proteins (IDPs), which are at the center of Alzheimer's and Parkinson's disease pathologies, respectively. These IDPs are extremely flexible and do not adopt stable structures. Furthermore, both amyloid-β and α-synuclein can form toxic oligomers, amyloid fibrils and other type of aggregates in Alzheimer's and Parkinson's diseases. Experimentalists face challenges in investigating the structures and thermodynamic properties of these IDPs in their monomeric and oligomeric forms due to the rapid conformational changes, fast aggregation processes and strong solvent effects. Classical molecular dynamics simulations complement experiments and provide structural information at the atomic level with dynamics without facing the same experimental limitations. Artificial missense mutations are employed experimentally and computationally for providing insights into the structure-function relationships of amyloid-β and α-synuclein in relation to the pathologies of Alzheimer's and Parkinson's diseases. Furthermore, there are several natural genetic variations that play a role in the pathogenesis of familial cases of Alzheimer's and Parkinson's diseases, which are related to specific genetic defects inherited in dominant or recessive patterns. The present review summarizes the current understanding of monomeric and oligomeric forms of amyloid-β and α-synuclein, as well as the impacts of artificial and pathological missense mutations on the structural ensembles of these IDPs using molecular dynamics simulations. We also emphasize the recent investigations on residual secondary structure formation in dynamic conformational ensembles of amyloid-β and α-synuclein, such as β-structure linked to the oligomerization and fibrillation mechanisms related to the pathologies of Alzheimer's and Parkinson's diseases. This information represents an important foundation for the successful and efficient drug design studies.
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Affiliation(s)
- Orkid Coskuner-Weber
- Türkisch-Deutsche Universität, Theoretical and Computational Biophysics Group, Molecular Biotechnology, Sahinkaya Caddesi, No. 86, Beykoz, Istanbul 34820, Turkey.
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
- Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia.
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14
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Qiang W, Doherty KE. Model Phospholipid Liposomes to Study the β-Amyloid-Peptide-Induced Membrane Disruption. Methods Mol Biol 2018; 1777:355-367. [PMID: 29744848 PMCID: PMC6298028 DOI: 10.1007/978-1-4939-7811-3_23] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
Model phospholipid liposomes have been utilized widely to study the molecular interactions between peptides and membrane bilayers. In the mechanistic study of Alzheimer's disease (AD), disruption of neuronal cell membranes has been considered as a major contribution for the β-amyloid (Aβ) peptides' neurotoxicity. However, clear interpretation of the Aβ-induced cellular membrane at high-resolution level is challenging because of the co-existence of multiple pathways. Here we present the generation of simplified model liposome systems that will facilitate the in-depth mechanistic studies. Protocols for the preparation of model liposomes and the characterization of individual membrane disruption effects will be described.
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Affiliation(s)
- Wei Qiang
- Department of Chemistry, State University of New York at Binghamton, Binghamton, NY, USA.
| | - Katelynne E Doherty
- Department of Chemistry, State University of New York at Binghamton, Binghamton, NY, USA
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15
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Hou S, Gu RX, Wei DQ. Inhibition of β-Amyloid Channels with a Drug Candidate wgx-50 Revealed by Molecular Dynamics Simulations. J Chem Inf Model 2017; 57:2811-2821. [DOI: 10.1021/acs.jcim.7b00452] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shuang Hou
- State
Key Laboratory of Microbial Metabolism and School of Life Sciences
and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ruo-Xu Gu
- Department
of Biological Sciences and Centre for Molecular Simulation, University of Calgary, 2500 University Dr. N.W., Calgary, AB T2N 1N4, Canada
| | - Dong-Qing Wei
- State
Key Laboratory of Microbial Metabolism and School of Life Sciences
and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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16
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Abstract
Previously published experimental studies have suggested that when the 40-residue amyloid beta peptide is encapsulated in a reverse micelle, it folds into a structure that may nucleate amyloid fibril formation (Yeung, P. S.-W.; Axelsen, P. H. J. Am. Chem. Soc. 2012, 134, 6061 ). The factors that induce the formation of this structure have now been identified in a multi-microsecond simulation of the same reverse micelle system that was studied experimentally. Key features of the polypeptide-micelle interaction include the anchoring of a hydrophobic residue cluster into gaps in the reverse micelle surface, the formation of a beta turn at the anchor point that brings N- and C-terminal segments of the polypeptide into proximity, high ionic strength that promotes intramolecular hydrogen bond formation, and deformation of the reverse micelle surface to facilitate interactions with the surface along the entire length of the polypeptide. Together, these features cause the simulation-derived vibrational spectrum to red shift in a manner that reproduces the red-shift previously reported experimentally. On the basis of these findings, a new mechanism is proposed whereby membranes nucleate fibril formation and facilitate the in-register alignment of polypeptide strands that is characteristic of amyloid fibrils.
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Affiliation(s)
- Gözde Eskici
- Department of Biochemistry & Biophysics, University of Pennsylvania Perelman School of Medicine , Philadelphia, Pennsylvania 19104, United States
| | - Paul H Axelsen
- Departments of Pharmacology, Biochemistry and Biophysics, and Medicine, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
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17
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Lee J, Kim YH, T Arce F, Gillman AL, Jang H, Kagan BL, Nussinov R, Yang J, Lal R. Amyloid β Ion Channels in a Membrane Comprising Brain Total Lipid Extracts. ACS Chem Neurosci 2017; 8:1348-1357. [PMID: 28135799 PMCID: PMC6197823 DOI: 10.1021/acschemneuro.7b00006] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Amyloid β (Aβ) oligomers are the predominant toxic species in the pathology of Alzheimer's disease. The prevailing mechanism for toxicity by Aβ oligomers includes ionic homeostasis destabilization in neuronal cells by forming ion channels. These channel structures have been previously studied in model lipid bilayers. In order to gain further insight into the interaction of Aβ oligomers with natural membrane compositions, we have examined the structures and conductivities of Aβ oligomers in a membrane composed of brain total lipid extract (BTLE). We utilized two complementary techniques: atomic force microscopy (AFM) and black lipid membrane (BLM) electrical recording. Our results indicate that Aβ1-42 forms ion channel structures in BTLE membranes, accompanied by a heterogeneous population of ionic current fluctuations. Notably, the observed current events generated by Aβ1-42 peptides in BTLE membranes possess different characteristics compared to current events generated by the presence of Aβ1-42 in model membranes comprising a 1:1 mixture of DOPS and POPE lipids. Oligomers of the truncated Aβ fragment Aβ17-42 (p3) exhibited similar ion conductivity behavior as Aβ1-42 in BTLE membranes. However, the observed macroscopic ion flux across the BTLE membranes induced by Aβ1-42 pores was larger than for p3 pores. Our analysis of structure and conductance of oligomeric Aβ pores in a natural lipid membrane closely mimics the in vivo cellular environment suggesting that Aβ pores could potentially accelerate the loss of ionic homeostasis and cellular abnormalities. Hence, these pore structures may serve as a target for drug development and therapeutic strategies for AD treatment.
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Affiliation(s)
| | | | - Fernando T Arce
- Division of Translational and Regenerative Medicine, Department of Medicine, Department of Biomedical Engineering, University of Arizona , Tucson, Arizona 85721, United States
| | | | - Hyunbum Jang
- Cancer and Inflammation Program, National Cancer Institute at Frederick, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Bruce L Kagan
- Department of Psychiatry, David Geffen School of Medicine, Semel Institute for Neuroscience and Human Behavior, University of California , Los Angeles, California 90024, United States
| | - Ruth Nussinov
- Cancer and Inflammation Program, National Cancer Institute at Frederick, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
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18
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Korshavn KJ, Satriano C, Lin Y, Zhang R, Dulchavsky M, Bhunia A, Ivanova MI, Lee YH, La Rosa C, Lim MH, Ramamoorthy A. Reduced Lipid Bilayer Thickness Regulates the Aggregation and Cytotoxicity of Amyloid-β. J Biol Chem 2017; 292:4638-4650. [PMID: 28154182 DOI: 10.1074/jbc.m116.764092] [Citation(s) in RCA: 136] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 01/31/2017] [Indexed: 11/06/2022] Open
Abstract
The aggregation of amyloid-β (Aβ) on lipid bilayers has been implicated as a mechanism by which Aβ exerts its toxicity in Alzheimer's disease (AD). Lipid bilayer thinning has been observed during both oxidative stress and protein aggregation in AD, but whether these pathological modifications of the bilayer correlate with Aβ misfolding is unclear. Here, we studied peptide-lipid interactions in synthetic bilayers of the short-chain lipid dilauroyl phosphatidylcholine (DLPC) as a simplified model for diseased bilayers to determine their impact on Aβ aggregate, protofibril, and fibril formation. Aβ aggregation and fibril formation in membranes composed of dioleoyl phosphatidylcholine (DOPC) or 1- palmitoyl-2-oleoyl phosphatidylcholine mimicking normal bilayers served as controls. Differences in aggregate formation and stability were monitored by a combination of thioflavin-T fluorescence, circular dichroism, atomic force microscopy, transmission electron microscopy, and NMR. Despite the ability of all three lipid bilayers to catalyze aggregation, DLPC accelerates aggregation at much lower concentrations and prevents the fibrillation of Aβ at low micromolar concentrations. DLPC stabilized globular, membrane-associated oligomers, which could disrupt the bilayer integrity. DLPC bilayers also remodeled preformed amyloid fibrils into a pseudo-unfolded, molten globule state, which resembled on-pathway, protofibrillar aggregates. Whereas the stabilized, membrane-associated oligomers were found to be nontoxic, the remodeled species displayed toxicity similar to that of conventionally prepared aggregates. These results provide mechanistic insights into the roles that pathologically thin bilayers may play in Aβ aggregation on neuronal bilayers, and pathological lipid oxidation may contribute to Aβ misfolding.
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Affiliation(s)
- Kyle J Korshavn
- From the Department of Chemistry.,Program in Biophysics, and
| | - Cristina Satriano
- the Department of Chemical Sciences, University of Catania, Catania 95124, Italy
| | - Yuxi Lin
- the Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | | | - Mark Dulchavsky
- Department of Neurology, University of Michigan, Ann Arbor, Michigan 48109
| | - Anirban Bhunia
- the Department of Biophysics, Bose Institute, Kolkata 700009, India, and
| | - Magdalena I Ivanova
- Program in Biophysics, and.,Department of Neurology, University of Michigan, Ann Arbor, Michigan 48109
| | - Young-Ho Lee
- the Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Carmelo La Rosa
- the Department of Chemical Sciences, University of Catania, Catania 95124, Italy
| | - Mi Hee Lim
- the Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
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19
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Gillman AL, Lee J, Ramachandran S, Capone R, Gonzalez T, Wrasidlo W, Masliah E, Lal R. Small molecule NPT-440-1 inhibits ionic flux through Aβ 1-42 pores: Implications for Alzheimer's disease therapeutics. NANOMEDICINE : NANOTECHNOLOGY, BIOLOGY, AND MEDICINE 2016; 12:2331-2340. [PMID: 27335341 PMCID: PMC5116404 DOI: 10.1016/j.nano.2016.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 05/31/2016] [Accepted: 06/04/2016] [Indexed: 12/11/2022]
Abstract
Increased levels of soluble amyloid-beta (Aβ) oligomers are suspected to underlie Alzheimer's disease (AD) pathophysiology. These oligomers have been shown to form multi-subunit Aβ pores in bilayers and induce uncontrolled, neurotoxic, ion flux, particularly calcium ions, across cellular membranes that might underlie cognitive impairment in AD. Small molecule interventions that modulate pore activity could effectively prevent or ameliorate their toxic activity. Here we examined the efficacy of a small molecule, NPT-440-1, on modulating amyloid pore permeability. Co-incubation of B103 rat neuronal cells with NPT-440-1 and Aβ1-42 prevented calcium influx. In purified lipid bilayers, we show that a 10-15min preincubation, prior to membrane introduction, was required to prevent conductance. Thioflavin-T and circular dichroism both suggested a reduction in Aβ1-42 β-sheet content during this incubation period. Combined with previous studies on site-specific amino acid substitutions, these results suggest that pharmacological modulation of Aβ1-42 could prevent amyloid pore-mediated AD pathogenesis.
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Affiliation(s)
- Alan L Gillman
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States
| | - Joon Lee
- Department of Mechanical and Aerospace Engineering University of California, San Diego, La Jolla, CA, United States
| | - Srinivasan Ramachandran
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States; Department of Mechanical and Aerospace Engineering University of California, San Diego, La Jolla, CA, United States
| | - Ricardo Capone
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, United States
| | - Tania Gonzalez
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, United States
| | - Wolf Wrasidlo
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, United States; Neuropore Therapies, Inc., San Diego, CA, United States
| | - Eliezer Masliah
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, United States.
| | - Ratnesh Lal
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States; Materials Science and Engineering Program, University of California, San Diego, La Jolla, CA, United States; Department of Mechanical and Aerospace Engineering University of California, San Diego, La Jolla, CA, United States.
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20
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Structure of amyloid oligomers and their mechanisms of toxicities: Targeting amyloid oligomers using novel therapeutic approaches. Eur J Med Chem 2016; 114:41-58. [DOI: 10.1016/j.ejmech.2016.02.065] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 02/25/2016] [Accepted: 02/25/2016] [Indexed: 01/22/2023]
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21
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Delgado DA, Doherty K, Cheng Q, Kim H, Xu D, Dong H, Grewer C, Qiang W. Distinct Membrane Disruption Pathways Are Induced by 40-Residue β-Amyloid Peptides. J Biol Chem 2016; 291:12233-44. [PMID: 27056326 DOI: 10.1074/jbc.m116.720656] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Indexed: 11/06/2022] Open
Abstract
Cellular membrane disruption induced by β-amyloid (Aβ) peptides has been considered one of the major pathological mechanisms for Alzheimer disease. Mechanistic studies of the membrane disruption process at a high-resolution level, on the other hand, are hindered by the co-existence of multiple possible pathways, even in simplified model systems such as the phospholipid liposome. Therefore, separation of these pathways is crucial to achieve an in-depth understanding of the Aβ-induced membrane disruption process. This study, which utilized a combination of multiple biophysical techniques, shows that the peptide-to-lipid (P:L) molar ratio is an important factor that regulates the selection of dominant membrane disruption pathways in the presence of 40-residue Aβ peptides in liposomes. Three distinct pathways (fibrillation with membrane content leakage, vesicle fusion, and lipid uptake through a temporarily stable ionic channel) become dominant in model liposome systems under specific conditions. These individual systems are characterized by both the initial states of Aβ peptides and the P:L molar ratio. Our results demonstrated the possibility to generate simplified Aβ-membrane model systems with a homogeneous membrane disruption pathway, which will benefit high-resolution mechanistic studies in the future. Fundamentally, the possibility of pathway selection controlled by P:L suggests that the driving forces for Aβ aggregation and Aβ-membrane interactions may be similar at the molecular level.
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Affiliation(s)
- Dennis A Delgado
- From the Department of Chemistry, State University of New York, Binghamton, New York 13902 and
| | - Katelynne Doherty
- From the Department of Chemistry, State University of New York, Binghamton, New York 13902 and
| | - Qinghui Cheng
- From the Department of Chemistry, State University of New York, Binghamton, New York 13902 and
| | - Hyeongeun Kim
- From the Department of Chemistry, State University of New York, Binghamton, New York 13902 and
| | - Dawei Xu
- the Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, New York 13699
| | - He Dong
- the Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, New York 13699
| | - Christof Grewer
- From the Department of Chemistry, State University of New York, Binghamton, New York 13902 and
| | - Wei Qiang
- From the Department of Chemistry, State University of New York, Binghamton, New York 13902 and
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22
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Jang H, Banerjee A, Chavan TS, Lu S, Zhang J, Gaponenko V, Nussinov R. The higher level of complexity of K-Ras4B activation at the membrane. FASEB J 2016; 30:1643-55. [PMID: 26718888 PMCID: PMC4799498 DOI: 10.1096/fj.15-279091] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 12/14/2015] [Indexed: 12/19/2022]
Abstract
Is nucleotide exchange sufficient to activate K-Ras4B? To signal, oncogenic rat sarcoma (Ras) anchors in the membrane and recruits effectors by exposing its effector lobe. With the use of NMR and molecular dynamics (MD) simulations, we observed that in solution, farnesylated guanosine 5'-diphosphate (GDP)-bound K-Ras4B is predominantly autoinhibited by its hypervariable region (HVR), whereas the GTP-bound state favors an activated, HVR-released state. On the anionic membrane, the catalytic domain adopts multiple orientations, including parallel (∼180°) and perpendicular (∼90°) alignments of the allosteric helices, with respect to the membrane surface direction. In the autoinhibited state, the HVR is sandwiched between the effector lobe and the membrane; in the active state, with membrane-anchored farnesyl and unrestrained HVR, the catalytic domain fluctuates reinlessly, exposing its effector-binding site. Dimerization and clustering can reduce the fluctuations. This achieves preorganized, productive conformations. Notably, we also observe HVR-autoinhibited K-Ras4B-GTP states, with GDP-bound-like orientations of the helices. Thus, we propose that the GDP/GTP exchange may not be sufficient for activation; instead, our results suggest that the GDP/GTP exchange, HVR sequestration, farnesyl insertion, and orientation/localization of the catalytic domain at the membrane conjointly determine the active or inactive state of K-Ras4B. Importantly, K-Ras4B-GTP can exist in active and inactive states; on its own, GTP binding may not compel K-Ras4B activation.-Jang, H., Banerjee, A., Chavan, T. S, Lu, S., Zhang, J., Gaponenko, V., Nussinov, R. The higher level of complexity of K-Ras4B activation at the membrane.
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Affiliation(s)
- Hyunbum Jang
- *Basic Science Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Cancer and Inflammation Program, National Cancer Institute at Frederick, Frederick, Maryland, USA; Department of Chemistry, Department of Medicinal Chemistry, and Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois, USA; Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis, Chinese Ministry of Education, Shanghai JiaoTong University, School of Medicine, Shanghai, China; and Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Avik Banerjee
- *Basic Science Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Cancer and Inflammation Program, National Cancer Institute at Frederick, Frederick, Maryland, USA; Department of Chemistry, Department of Medicinal Chemistry, and Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois, USA; Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis, Chinese Ministry of Education, Shanghai JiaoTong University, School of Medicine, Shanghai, China; and Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Tanmay S Chavan
- *Basic Science Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Cancer and Inflammation Program, National Cancer Institute at Frederick, Frederick, Maryland, USA; Department of Chemistry, Department of Medicinal Chemistry, and Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois, USA; Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis, Chinese Ministry of Education, Shanghai JiaoTong University, School of Medicine, Shanghai, China; and Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Shaoyong Lu
- *Basic Science Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Cancer and Inflammation Program, National Cancer Institute at Frederick, Frederick, Maryland, USA; Department of Chemistry, Department of Medicinal Chemistry, and Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois, USA; Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis, Chinese Ministry of Education, Shanghai JiaoTong University, School of Medicine, Shanghai, China; and Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Jian Zhang
- *Basic Science Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Cancer and Inflammation Program, National Cancer Institute at Frederick, Frederick, Maryland, USA; Department of Chemistry, Department of Medicinal Chemistry, and Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois, USA; Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis, Chinese Ministry of Education, Shanghai JiaoTong University, School of Medicine, Shanghai, China; and Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Vadim Gaponenko
- *Basic Science Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Cancer and Inflammation Program, National Cancer Institute at Frederick, Frederick, Maryland, USA; Department of Chemistry, Department of Medicinal Chemistry, and Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois, USA; Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis, Chinese Ministry of Education, Shanghai JiaoTong University, School of Medicine, Shanghai, China; and Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ruth Nussinov
- *Basic Science Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Cancer and Inflammation Program, National Cancer Institute at Frederick, Frederick, Maryland, USA; Department of Chemistry, Department of Medicinal Chemistry, and Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois, USA; Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis, Chinese Ministry of Education, Shanghai JiaoTong University, School of Medicine, Shanghai, China; and Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
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23
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Arbor SC, LaFontaine M, Cumbay M. Amyloid-beta Alzheimer targets - protein processing, lipid rafts, and amyloid-beta pores. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2016; 89:5-21. [PMID: 27505013 PMCID: PMC4797837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Amyloid beta (Aβ), the hallmark of Alzheimer's Disease (AD), now appears to be deleterious in its low number aggregate form as opposed to the macroscopic Aβ fibers historically seen postmortem. While Alzheimer targets, such as the tau protein, amyloid precursor protein (APP) processing, and immune system activation continue to be investigated, the recent discovery that amyloid beta aggregates at lipid rafts and likely forms neurotoxic pores has led to a new paradigm regarding why past therapeutics may have failed and how to design the next round of compounds for clinical trials. An atomic resolution understanding of Aβ aggregates, which appear to exist in multiple conformations, is most desirable for future therapeutic development. The investigative difficulties, structures of these small Aβ aggregates, and current therapeutics are summarized in this review.
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Affiliation(s)
- Sage C. Arbor
- Marian University College of Osteopathic Medicine, 3200 Cold Spring Road, Indianapolis, Indiana, 46222
| | - Mike LaFontaine
- Marian University College of Osteopathic Medicine, 3200 Cold Spring Road, Indianapolis, Indiana, 46222
| | - Medhane Cumbay
- Marian University College of Osteopathic Medicine, 3200 Cold Spring Road, Indianapolis, Indiana, 46222
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24
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Jang H, Arce FT, Lee J, Gillman AL, Ramachandran S, Kagan BL, Lal R, Nussinov R. Computational Methods for Structural and Functional Studies of Alzheimer's Amyloid Ion Channels. Methods Mol Biol 2016; 1345:251-68. [PMID: 26453217 PMCID: PMC7511997 DOI: 10.1007/978-1-4939-2978-8_16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Aggregation can be studied by a range of methods, experimental and computational. Aggregates form in solution, across solid surfaces, and on and in the membrane, where they may assemble into unregulated leaking ion channels. Experimental probes of ion channel conformations and dynamics are challenging. Atomistic molecular dynamics (MD) simulations are capable of providing insight into structural details of amyloid ion channels in the membrane at a resolution not achievable experimentally. Since data suggest that late stage Alzheimer's disease involves formation of toxic ion channels, MD simulations have been used aiming to gain insight into the channel shapes, morphologies, pore dimensions, conformational heterogeneity, and activity. These can be exploited for drug discovery. Here we describe computational methods to model amyloid ion channels containing the β-sheet motif at atomic scale and to calculate toxic pore activity in the membrane.
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Affiliation(s)
- Hyunbum Jang
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, 1050 Boyles Street, Frederick, MD, 21702, USA.
| | - Fernando Teran Arce
- Department of Bioengineering, Materials Science Program, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Mechanical and Aerospace Engineering, Materials Science Program, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Joon Lee
- Department of Mechanical and Aerospace Engineering, Materials Science Program, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Alan L Gillman
- Department of Bioengineering, Materials Science Program, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Srinivasan Ramachandran
- Department of Bioengineering, Materials Science Program, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Mechanical and Aerospace Engineering, Materials Science Program, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Bruce L Kagan
- Department of Psychiatry, David Geffen School of Medicine, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, 90024, USA
| | - Ratnesh Lal
- Department of Bioengineering, Materials Science Program, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Mechanical and Aerospace Engineering, Materials Science Program, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, 1050 Boyles Street, Frederick, MD, 21702, USA.
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel.
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25
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Patel N, Ramachandran S, Azimov R, Kagan BL, Lal R. Ion Channel Formation by Tau Protein: Implications for Alzheimer's Disease and Tauopathies. Biochemistry 2015; 54:7320-5. [PMID: 26575330 PMCID: PMC4690196 DOI: 10.1021/acs.biochem.5b00988] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
![]()
Tau
is a microtubule associated protein implicated in the pathogenesis
of several neurodegenerative diseases. Because of the channel forming
properties of other amyloid peptides, we employed planar lipid bilayers
and atomic force microscopy to test tau for its ability to form ion
permeable channels. Our results demonstrate that tau can form such
channels, but only under acidic conditions. The channels formed are
remarkably similar to amyloid peptide channels in their appearance,
physical and electrical size, permanence, lack of ion selectivity,
and multiple channel conductances. These channels differ from amyloid
channels in their voltage dependence and resistance to blockade by
zinc ion. These channels could explain tau’s pathologic role
in disease by lowering membrane potential, dysregulating calcium,
depolarizing mitochondria, or depleting energy stores. Tau might also
combine with amyloid beta peptides to form toxic channels.
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Affiliation(s)
- Nirav Patel
- Departments of Bioengineering and Mechanical & Aerospace Engineering, University of California at San Diego , La Jolla, California 92093, United States
| | - Srinivasan Ramachandran
- Departments of Bioengineering and Mechanical & Aerospace Engineering, University of California at San Diego , La Jolla, California 92093, United States
| | - Rustam Azimov
- Department of Psychiatry, David Geffen School of Medicine, Semel Institute for Neuroscience & Human Behavior, University of California , Los Angeles, California 90095, United States
| | - Bruce L Kagan
- Department of Psychiatry, David Geffen School of Medicine, Semel Institute for Neuroscience & Human Behavior, University of California , Los Angeles, California 90095, United States
| | - Ratnesh Lal
- Departments of Bioengineering and Mechanical & Aerospace Engineering, University of California at San Diego , La Jolla, California 92093, United States
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26
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Jang H, Abraham SJ, Chavan TS, Hitchinson B, Khavrutskii L, Tarasova NI, Nussinov R, Gaponenko V. Mechanisms of membrane binding of small GTPase K-Ras4B farnesylated hypervariable region. J Biol Chem 2015; 290:9465-77. [PMID: 25713064 PMCID: PMC4392252 DOI: 10.1074/jbc.m114.620724] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 02/19/2015] [Indexed: 01/08/2023] Open
Abstract
K-Ras4B belongs to a family of small GTPases that regulates cell growth, differentiation and survival. K-ras is frequently mutated in cancer. K-Ras4B association with the plasma membrane through its farnesylated and positively charged C-terminal hypervariable region (HVR) is critical to its oncogenic function. However, the structural mechanisms of membrane association are not fully understood. Here, using confocal microscopy, surface plasmon resonance, and molecular dynamics simulations, we observed that K-Ras4B can be distributed in rigid and loosely packed membrane domains. Its membrane binding domain interaction with phospholipids is driven by membrane fluidity. The farnesyl group spontaneously inserts into the disordered lipid microdomains, whereas the rigid microdomains restrict the farnesyl group penetration. We speculate that the resulting farnesyl protrusion toward the cell interior allows oligomerization of the K-Ras4B membrane binding domain in rigid microdomains. Unlike other Ras isoforms, K-Ras4B HVR contains a single farnesyl modification and positively charged polylysine sequence. The high positive charge not only modulates specific HVR binding to anionic phospholipids but farnesyl membrane orientation. Phosphorylation of Ser-181 prohibits spontaneous farnesyl membrane insertion. The mechanism illuminates the roles of HVR modifications in K-Ras4B targeting microdomains of the plasma membrane and suggests an additional function for HVR in regulation of Ras signaling.
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Affiliation(s)
- Hyunbum Jang
- From the Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research and Cancer and Inflammation Program, NCI-Frederick, National Institutes of Health, Frederick, Maryland 21702
| | - Sherwin J Abraham
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, California 94305, Departments of Biochemistry and Molecular Genetics and
| | - Tanmay S Chavan
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, California 94305, Medicinal Chemistry, University of Illinois, Chicago, Illinois 60607, and
| | | | - Lyuba Khavrutskii
- From the Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research and Cancer and Inflammation Program, NCI-Frederick, National Institutes of Health, Frederick, Maryland 21702
| | - Nadya I Tarasova
- Cancer and Inflammation Program, NCI-Frederick, National Institutes of Health, Frederick, Maryland 21702,
| | - Ruth Nussinov
- From the Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research and Cancer and Inflammation Program, NCI-Frederick, National Institutes of Health, Frederick, Maryland 21702, Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Vadim Gaponenko
- Departments of Biochemistry and Molecular Genetics and Medicinal Chemistry, University of Illinois, Chicago, Illinois 60607, and
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27
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Qiang W, Akinlolu RD, Nam M, Shu N. Structural evolution and membrane interaction of the 40-residue β amyloid peptides: differences in the initial proximity between peptides and the membrane bilayer studied by solid-state nuclear magnetic resonance spectroscopy. Biochemistry 2014; 53:7503-14. [PMID: 25397729 DOI: 10.1021/bi501003n] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Interactions between the β amyloid (Aβ) peptides and cellular membranes have severe consequences such as neuronal cell disruption and therefore may play important roles in Alzheimer's disease. Understanding the structural basis behind such interactions, however, is hindered by the complexity of the Aβ-membrane systems. In particular, because the Aβ peptides are partially incorporated in the membrane bilayer after enzymatic cleavage, there are multiple possibilities in terms of the initial proximity between the peptides and membranes. Structural studies using in vitro model systems with either externally added or preincorporated Aβ in membrane bilayers resulted in distinct evolution pathways. Previous work has shown that the externally added Aβ formed long and mature filaments, while preincorporated Aβ generated short and curvy fibrils. In this study, we perform detailed characterizations on the structural evolution and membrane interaction for these two pathways, using a combination of solid-state nuclear magnetic resonance spectroscopy and other techniques. For the externally added Aβ, we determined the residue-specific structural evolution during the fibrillation process. While the entire fibrillation process for the externally added Aβ was slow, the preincorporated Aβ generated Aβ-lipid complexes rapidly. Specific interactions between the lipids and peptides were observed, suggesting the colocalization of lipids and peptides within the complex. Formation of such a complex induced molecular-level changes in the lipid bilayer, which may serve as a possible mechanism of membrane disruption.
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Affiliation(s)
- Wei Qiang
- Department of Chemistry, Binghamton University, State University of New York , Binghamton, New York 13902, United States
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28
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Jang H, Arce FT, Ramachandran S, Kagan BL, Lal R, Nussinov R. Disordered amyloidogenic peptides may insert into the membrane and assemble into common cyclic structural motifs. Chem Soc Rev 2014; 43:6750-64. [PMID: 24566672 PMCID: PMC4143503 DOI: 10.1039/c3cs60459d] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Aggregation of disordered amyloidogenic peptides into oligomers is the causative agent of amyloid-related diseases. In solution, disordered protein states are characterized by heterogeneous ensembles. Among these, β-rich conformers self-assemble via a conformational selection mechanism to form energetically-favored cross-β structures, regardless of their precise sequences. These disordered peptides can also penetrate the membrane, and electrophysiological data indicate that they form ion-conducting channels. Based on these and additional data, including imaging and molecular dynamics simulations of a range of amyloid peptides, Alzheimer's amyloid-β (Aβ) peptide, its disease-related variants with point mutations and N-terminal truncated species, other amyloidogenic peptides, as well as a cytolytic peptide and a synthetic gel-forming peptide, we suggest that disordered amyloidogenic peptides can also present a common motif in the membrane. The motif consists of curved, moon-like β-rich oligomers associated into annular organizations. The motif is favored in the lipid bilayer since it permits hydrophobic side chains to face and interact with the membrane and the charged/polar residues to face the solvated channel pores. Such channels are toxic since their pores allow uncontrolled leakage of ions into/out of the cell, destabilizing cellular ionic homeostasis. Here we detail Aβ, whose aggregation is associated with Alzheimer's disease (AD) and for which there are the most abundant data. AD is a protein misfolding disease characterized by a build-up of Aβ peptide as senile plaques, neurodegeneration, and memory loss. Excessively produced Aβ peptides may directly induce cellular toxicity, even without the involvement of membrane receptors through Aβ peptide-plasma membrane interactions.
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Affiliation(s)
- Hyunbum Jang
- Cancer and Inflammation Program, National Cancer Institute at Frederick, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, U.S.A
| | - Fernando Teran Arce
- Departments of Bioengineering and of Mechanical and Aerospace Engineering, and Materials Science Program, University of California, San Diego, La Jolla, California 92093, U.S.A
| | - Srinivasan Ramachandran
- Departments of Bioengineering and of Mechanical and Aerospace Engineering, and Materials Science Program, University of California, San Diego, La Jolla, California 92093, U.S.A
| | - Bruce L. Kagan
- Department of Psychiatry, David Geffen School of Medicine, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, California 90024, U.S.A
| | - Ratnesh Lal
- Departments of Bioengineering and of Mechanical and Aerospace Engineering, and Materials Science Program, University of California, San Diego, La Jolla, California 92093, U.S.A
| | - Ruth Nussinov
- Cancer and Inflammation Program, National Cancer Institute at Frederick, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, U.S.A
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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29
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Zhao J, Hu R, Sciacca MFM, Brender JR, Chen H, Ramamoorthy A, Zheng J. Non-selective ion channel activity of polymorphic human islet amyloid polypeptide (amylin) double channels. Phys Chem Chem Phys 2014; 16:2368-77. [PMID: 24352606 DOI: 10.1039/c3cp53345j] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fundamental understanding of ion channel formation by amyloid peptides, which is strongly linked to cell toxicity, is very critical for (pre)clinical treatment of neurodegenerative diseases. Here, we combine atomistic simulations and experiments to demonstrate a broad range of conformational states of hIAPP double channels in lipid membranes. All individual channels display high selectivity for Cl(-) ions over cations, but the co-existence of polymorphic double channels of different conformations and orientations with different populations determines the non-ionic selectivity nature of the channels, which is different from the typical amyloid-β channels that exhibit Ca(2+) selective ion-permeable characteristics. This work provides a more complete physicochemical mechanism of amyloid-channel-induced toxicity.
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Affiliation(s)
- Jun Zhao
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, OH 44325, USA.
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30
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Lee J, Gillman AL, Jang H, Ramachandran S, Kagan BL, Nussinov R, Teran Arce F. Role of the fast kinetics of pyroglutamate-modified amyloid-β oligomers in membrane binding and membrane permeability. Biochemistry 2014; 53:4704-14. [PMID: 24950761 PMCID: PMC4215883 DOI: 10.1021/bi500587p] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
![]()
Membrane
permeability to ions and small molecules is believed to
be a critical step in the pathology of Alzheimer’s disease
(AD). Interactions of oligomers formed by amyloid-β (Aβ)
peptides with the plasma cell membrane are believed to play a fundamental
role in the processes leading to membrane permeability. Among the
family of Aβs, pyroglutamate (pE)-modified Aβ peptides
constitute the most abundant oligomeric species in the brains of AD
patients. Although membrane permeability mechanisms have been studied
for full-length Aβ1–40/42 peptides, these
have not been sufficiently characterized for the more abundant AβpE3–42 fragment. Here we have compared the adsorbed
and membrane-inserted oligomeric species of AβpE3–42 and Aβ1–42 peptides. We find lower concentrations
and larger dimensions for both species of membrane-associated AβpE3–42 oligomers. The larger dimensions are attributed
to the faster self-assembly kinetics of AβpE3–42, and the lower concentrations are attributed to weaker interactions
with zwitterionic lipid headgroups. While adsorbed oligomers produced
little or no significant membrane structural damage, increased membrane
permeabilization to ionic species is understood in terms of enlarged
membrane-inserted oligomers. Membrane-inserted AβpE3–42 oligomers were also found to modify the mechanical properties of
the membrane. Taken together, our results suggest that membrane-inserted
oligomers are the primary species responsible for membrane permeability.
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Affiliation(s)
- Joon Lee
- Department of Bioengineering, University of California at San Diego , La Jolla, California 92093, United States
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31
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Gillman AL, Jang H, Lee J, Ramachandran S, Kagan B, Nussinov R, Teran Arce F. Activity and architecture of pyroglutamate-modified amyloid-β (AβpE3-42) pores. J Phys Chem B 2014; 118:7335-44. [PMID: 24922585 PMCID: PMC4096221 DOI: 10.1021/jp5040954] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2014] [Revised: 06/10/2014] [Indexed: 12/17/2022]
Abstract
Among the family of Aβ peptides, pyroglutamate-modified Aβ (AβpE) peptides are particularly associated with cytotoxicity in Alzheimer's disease (AD). They represent the dominant fraction of Aβ oligomers in the brains of AD patients, but their accumulation in the brains of elderly individuals with normal cognition is significantly lower. Accumulation of AβpE plaques precedes the formation of plaques of full-length Aβ (Aβ1-40/42). Most of these properties appear to be associated with the higher hydrophobicity of AβpE as well as an increased resistance to enzymatic degradation. However, the important question of whether AβpE peptides induce pore activity in lipid membranes and their potential toxicity compared with other Aβ pores is still open. Here we examine the activity of AβpE pores in anionic membranes using planar bilayer electrical recording and provide their structures using molecular dynamics simulations. We find that AβpE pores spontaneously induce ionic current across the membrane and have some similar properties to the other previously studied pores of the Aβ family. However, there are also some significant differences. The onset of AβpE3-42 pore activity is generally delayed compared with Aβ1-42 pores. However, once formed, AβpE3-42 pores produce increased ion permeability of the membrane, as indicated by a greater occurrence of higher conductance electrical events. Structurally, the lactam ring of AβpE peptides induces a change in the conformation of the N-terminal strands of the AβpE3-42 pores. While the N-termini of wild-type Aβ1-42 peptides normally reside in the bulk water region, the N-termini of AβpE3-42 peptides tend to reside in the hydrophobic lipid core. These studies provide a first step to an understanding of the enhanced toxicity attributed to AβpE peptides.
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Affiliation(s)
- Alan L. Gillman
- Department
of Bioengineering, University of California,
San Diego, 9500 Gilman
Drive, La Jolla, California 92093, United States
| | - Hyunbum Jang
- Cancer
and Inflammation Program, National Cancer Institute at Frederick,
Leidos Biomedical Research, Inc., Frederick
National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Joon Lee
- Department
of Mechanical and Aerospace Engineering and Material Science Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Srinivasan Ramachandran
- Department
of Bioengineering, University of California,
San Diego, 9500 Gilman
Drive, La Jolla, California 92093, United States
- Department
of Mechanical and Aerospace Engineering and Material Science Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Bruce
L. Kagan
- Department
of Psychiatry, David Geffen School of Medicine, Semel Institute for
Neuroscience and Human Behavior, University
of California, 760 Westwood
Plaza, Los Angeles, California 90024, United States
| | - Ruth Nussinov
- Cancer
and Inflammation Program, National Cancer Institute at Frederick,
Leidos Biomedical Research, Inc., Frederick
National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
- Department
of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Fernando Teran Arce
- Department
of Bioengineering, University of California,
San Diego, 9500 Gilman
Drive, La Jolla, California 92093, United States
- Department
of Mechanical and Aerospace Engineering and Material Science Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
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32
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Morriss-Andrews A, Brown FLH, Shea JE. A coarse-grained model for peptide aggregation on a membrane surface. J Phys Chem B 2014; 118:8420-32. [PMID: 24791936 DOI: 10.1021/jp502871m] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The aggregation of peptides on a lipid bilayer is studied using coarse-grained molecular dynamics in implicit solvent. Peptides bind to and self-assemble on the membrane surface into β-rich fibrillar aggregates, even under conditions where only disordered oligomers form in bulk solution. Relative to a solid surface, the membrane surface facilitates peptide mobility and a more complex network of morphology transitions as aggregation proceeds. Additionally, final aggregate structures realized on the membrane surface are distinct from those observed on a comparable solid surface. The aggregated fibrils alter the local structure and material properties of the lipid bilayer in their immediate vicinity but have only a modest effect on the overall bending rigidity of the bilayer.
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Affiliation(s)
- Alex Morriss-Andrews
- Department of Physics, University of California Santa Barbara , Santa Barbara, California 93106, United States
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33
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Connelly LS, Meckes B, Larkin J, Gillman AL, Wanunu M, Lal R. Graphene nanopore support system for simultaneous high-resolution AFM imaging and conductance measurements. ACS APPLIED MATERIALS & INTERFACES 2014; 6:5290-6. [PMID: 24581087 PMCID: PMC4232248 DOI: 10.1021/am500639q] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 02/28/2014] [Indexed: 05/24/2023]
Abstract
Accurately defining the nanoporous structure and sensing the ionic flow across nanoscale pores in thin films and membranes has a wide range of applications, including characterization of biological ion channels and receptors, DNA sequencing, molecule separation by nanoparticle films, sensing by block co-polymers films, and catalysis through metal-organic frameworks. Ionic conductance through nanopores is often regulated by their 3D structures, a relationship that can be accurately determined only by their simultaneous measurements. However, defining their structure-function relationships directly by any existing techniques is still not possible. Atomic force microscopy (AFM) can image the structures of these pores at high resolution in an aqueous environment, and electrophysiological techniques can measure ion flow through individual nanoscale pores. Combining these techniques is limited by the lack of nanoscale interfaces. We have designed a graphene-based single-nanopore support (∼5 nm thick with ∼20 nm pore diameter) and have integrated AFM imaging and ionic conductance recording using our newly designed double-chamber recording system to study an overlaid thin film. The functionality of this integrated system is demonstrated by electrical recording (<10 pS conductance) of suspended lipid bilayers spanning a nanopore and simultaneous AFM imaging of the bilayer.
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Affiliation(s)
- Laura S. Connelly
- Materials Science and Engineering
Program, Department of Bioengineering, and Department of Mechanical and Aerospace Engineering, University of California−San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Brian Meckes
- Materials Science and Engineering
Program, Department of Bioengineering, and Department of Mechanical and Aerospace Engineering, University of California−San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Joseph Larkin
- Department of Physics, Northeastern University, 110 Forsyth Street, Boston, Massachusetts 02115, United States
| | - Alan L. Gillman
- Materials Science and Engineering
Program, Department of Bioengineering, and Department of Mechanical and Aerospace Engineering, University of California−San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Meni Wanunu
- Department of Physics, Northeastern University, 110 Forsyth Street, Boston, Massachusetts 02115, United States
| | - Ratnesh Lal
- Materials Science and Engineering
Program, Department of Bioengineering, and Department of Mechanical and Aerospace Engineering, University of California−San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
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34
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Hayden EY, Teplow DB. Amyloid β-protein oligomers and Alzheimer's disease. ALZHEIMERS RESEARCH & THERAPY 2013; 5:60. [PMID: 24289820 PMCID: PMC3978746 DOI: 10.1186/alzrt226] [Citation(s) in RCA: 192] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The oligomer cascade hypothesis, which states that oligomers are the initiating pathologic agents in Alzheimer’s disease, has all but supplanted the amyloid cascade hypothesis, which suggested that fibers were the key etiologic agents in Alzheimer’s disease. We review here the results of in vivo, in vitro and in silico studies of amyloid β-protein oligomers, and discuss important caveats that should be considered in the evaluation of these results. This article is divided into four sections that mirror the main approaches used in the field to better understand oligomers: (1) attempts to locate and examine oligomers in vivo in situ; that is, without removing these species from their environment; (2) studies involving oligomers extracted from human or animal tissues and the subsequent characterization of their properties ex vivo; (3) studies of oligomers that have been produced synthetically and studied using a reductionist approach in relatively simple in vitro biophysical systems; and (4) computational studies of oligomers in silico. These multiple orthogonal approaches have revealed much about the molecular and cell biology of amyloid β-protein. However, as informative as these approaches have been, the amyloid β-protein oligomer system remains enigmatic.
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Affiliation(s)
- Eric Y Hayden
- Department of Neurology, 635 Charles E. Young Drive South, Room 455, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - David B Teplow
- Department of Neurology, 635 Charles E. Young Drive South, Room 455, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA ; Brain Research and Molecular Biology Institutes, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
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35
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Jang H, Arce FT, Ramachandran S, Kagan BL, Lal R, Nussinov R. Familial Alzheimer's disease Osaka mutant (ΔE22) β-barrels suggest an explanation for the different Aβ1-40/42 preferred conformational states observed by experiment. J Phys Chem B 2013; 117:11518-29. [PMID: 24000923 PMCID: PMC3946471 DOI: 10.1021/jp405389n] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An unusual ΔE693 mutation in the amyloid precursor protein (APP) producing a β-amyloid (Aβ) peptide lacking glutamic acid at position 22 (Glu22) was recently discovered, and dabbed the Osaka mutant (ΔE22). Previously, several point mutations in the Aβ peptide involving Glu22 substitutions were identified and implicated in the early onset of familial Alzheimer's disease (FAD). Despite the absence of Glu22, the Osaka mutant is also associated with FAD, showing a recessive inheritance in families affected by the disease. To see whether this aggregation-prone Aβ mutant could directly relate to the Aβ ion channel-mediated mechanism as observed for the wild type (WT) Aβ peptide in AD pathology, we modeled Osaka mutant β-barrels in a lipid bilayer. Using molecular dynamics (MD) simulations, two conformer ΔE22 barrels with the U-shaped monomer conformation derived from NMR-based WT Aβ fibrils were simulated in explicit lipid environment. Here, we show that the ΔE22 barrels obtain the lipid-relaxed β-sheet channel topology, indistinguishable from the WT Aβ1-42 barrels, as do the outer and pore dimensions of octadecameric (18-mer) ΔE22 barrels. Although the ΔE22 barrels lose the cationic binding site in the pore which is normally provided by the negatively charged Glu22 side chains, the mutant pores gain a new cationic binding site by Glu11 at the lower bilayer leaflet, and exhibit ion fluctuations similar to the WT barrels. Of particular interest, this deletion mutant suggests that toxic WT Aβ1-42 would preferentially adopt a less C-terminal turn similar to that observed for Aβ17-42, and explains why the solid state NMR data for Aβ1-40 point to a more C-terminal turn conformation. The observed ΔE22 barrels conformational preferences also suggest an explanation for the lower neurotoxicity in rat primary neurons as compared to WT Aβ1-42.
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Affiliation(s)
- Hyunbum Jang
- Basic Science Program, SAIC-Frederick, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, USA
| | - Fernando Teran Arce
- Departments of Bioengineering and of Mechanical and Aerospace Engineering, and Materials Science Program, University of California, San Diego, La Jolla, California 92093, USA
| | - Srinivasan Ramachandran
- Departments of Bioengineering and of Mechanical and Aerospace Engineering, and Materials Science Program, University of California, San Diego, La Jolla, California 92093, USA
| | - Bruce L. Kagan
- Department of Psychiatry, David Geffen School of Medicine, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, California 90024, USA
| | - Ratnesh Lal
- Departments of Bioengineering and of Mechanical and Aerospace Engineering, and Materials Science Program, University of California, San Diego, La Jolla, California 92093, USA
| | - Ruth Nussinov
- Basic Science Program, SAIC-Frederick, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, USA
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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36
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Microsecond molecular dynamics simulation of Aβ42 and identification of a novel dual inhibitor of Aβ42 aggregation and BACE1 activity. Acta Pharmacol Sin 2013; 34:1243-50. [PMID: 23770985 DOI: 10.1038/aps.2013.55] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 04/10/2013] [Indexed: 12/17/2022] Open
Abstract
AIM To study the conformational changes of Aβ42 and discover novel inhibitors of both Aβ42 aggregation and β-secretase (BACE1). METHODS A molecular dynamics (MD) simulation at a microsecond level was performed to explore stable conformations of Aβ42 monomer in aqueous solution. Subsequently, structure-based virtual screening was used to search for inhibitors of both Aβ42 aggregation and BACE1. Protein purification and in vitro activity assays were performed to validate the inhibition of the compounds identified via virtual screening. RESULTS The initial α-helical conformation of Aβ42, which was unstable in aqueous solution, turned into a β-sheet mixed with a coil structure through a transient and fully random coil. The conformation of Aβ42 mainly comprising β-sheets and coils structure was used for further virtual screening. Five compounds were identified as inhibitors for Aβ42 aggregation, and one of them, AE-848, was discovered to be a dual inhibitor of both Aβ42 aggregation and BACE1, with IC50 values of 36.95 μmol/L and 22.70 μmol/L, respectively. CONCLUSION A helical to β-sheet conformational change in Aβ42 occurred in a 1.8 microsecond MD simulation. The resulting β-sheet structure of the peptide is an appropriate conformation for the virtual screening of inhibitors against Aβ42 aggregation. Five compounds were identified as inhibitors of Aβ42 aggregation by in vitro activity assays. It was particularly interesting to discover a dual inhibitor that targets both Aβ42 aggregation and BACE1, the two crucial players in the pathogenesis of Alzheimer's disease.
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Jang H, Connelly L, Arce FT, Ramachandran S, Lal R, Kagan BL, Nussinov R. Alzheimer's disease: which type of amyloid-preventing drug agents to employ? Phys Chem Chem Phys 2013; 15:8868-77. [PMID: 23450150 PMCID: PMC3663909 DOI: 10.1039/c3cp00017f] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The current paradigm in the amyloid hypothesis brands small β-amyloid (Aβ) oligomers as the toxic species in Alzheimer's disease (AD). These oligomers are fibril-like; contain β-sheet structure, and present exposed hydrophobic surface. Oligomers with this motif are capable of penetrating the cell membrane, gathering to form toxic ion channels. Current agents suppressing precursor Aβ cleavage have only met partial success; and to date, those targeting the peptides and their assemblies in the aqueous environment of the extracellular space largely fail in clinical trials. One possible reason is failure to reach membrane-embedded targets of disease-'infected' cells. Here we provide an overview, point to the need to account for the lipid environment when aiming to prevent the formation of toxic channels, and propose a combination therapy to target the species spectrum.
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Affiliation(s)
- Hyunbum Jang
- Center for Cancer Research, Nanobiology Program, Basic Science Program, SAIC-Frederick, Inc., National Cancer Institute, Frederick, Maryland 21702, USA
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Abstract
Alzheimer's disease (AD) is an urgent public health challenge that is rapidly approaching epidemic proportions. New therapies that defer or prevent the onset, delay the decline, or improve the symptoms are urgently needed. All phase 3 drug development programs for disease-modifying agents have failed thus far. New approaches to drug development are needed. Translational neuroscience focuses on the linkages between basic neuroscience and the development of new diagnostic and therapeutic products that will improve the lives of patients or prevent the occurrence of brain disorders. Translational neuroscience includes new preclinical models that may better predict human efficacy and safety, improved clinical trial designs and outcomes that will accelerate drug development, and the use of biomarkers to more rapidly provide information regarding the effects of drugs on the underlying disease biology. Early translational research is complemented by later stage translational approaches regarding how best to use evidence to impact clinical practice and to assess the influence of new treatments on the public health. Funding of translational research is evolving with an increased emphasis on academic and NIH involvement in drug development. Translational neuroscience provides a framework for advancing development of new therapies for AD patients.
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Yates EA, Owens SL, Lynch MF, Cucco EM, Umbaugh CS, Legleiter J. Specific domains of Aβ facilitate aggregation on and association with lipid bilayers. J Mol Biol 2013; 425:1915-1933. [PMID: 23524134 DOI: 10.1016/j.jmb.2013.03.022] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 02/09/2013] [Accepted: 03/04/2013] [Indexed: 11/27/2022]
Abstract
A hallmark of Alzheimer's disease, a late-onset neurodegenerative disease, is the deposition of neuritic amyloid plaques composed of aggregated forms of the β-amyloid peptide (Aβ). Aβ forms a variety of nanoscale, toxic aggregate species ranging from small oligomers to fibrils. Aβ and many of its aggregate forms strongly interact with lipid membranes, which may represent an important step in several toxic mechanisms. Understanding the role that specific regions of Aβ play in regulating its aggregation and interaction with lipid membranes may provide insights into the fundamental interaction between Aβ and cellular surfaces. We investigated the interaction and aggregation of several Aβ fragments (Aβ1-11, Aβ1-28, Aβ10-26, Aβ12-24, Aβ16-22, Aβ22-35, and Aβ1-40) in the presence of supported model total brain lipid extract (TBLE) bilayers. These fragments represent a variety of chemically unique domains within Aβ, that is, the extracellular domain, the central hydrophobic core, and the transmembrane domain. Using scanning probe techniques, we elucidated aggregate morphologies for these different Aβ fragments in free solution and in the presence of TBLE bilayers. These fragments formed a variety of oligomeric and fibrillar aggregates under free solution conditions. Exposure to TBLE bilayers resulted in distinct aggregate morphologies compared to free solution and changes in bilayer stability dependent on the Aβ sequence. Aβ10-26, Aβ16-22, Aβ22-35, and Aβ1-40 aggregated into a variety of distinct fibrillar aggregates and disrupted the bilayer structure, resulting in altered mechanical properties of the bilayer. Aβ1-11, Aβ1-28, and Aβ12-24 had minimal interaction with lipid membranes, forming only sparse oligomers.
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Affiliation(s)
- Elizabeth A Yates
- The C. Eugene Bennett Department of Chemistry, 217 Clark Hall, West Virginia University, Morgantown, WV 26506, USA
| | - Sherry L Owens
- The C. Eugene Bennett Department of Chemistry, 217 Clark Hall, West Virginia University, Morgantown, WV 26506, USA
| | - Michael F Lynch
- The C. Eugene Bennett Department of Chemistry, 217 Clark Hall, West Virginia University, Morgantown, WV 26506, USA
| | - Elena M Cucco
- Center for Neuroscience, Robert C. Byrd Health Sciences Center, PO Box 9304, West Virginia University, Morgantown, WV 26506, USA
| | - C Samuel Umbaugh
- The C. Eugene Bennett Department of Chemistry, 217 Clark Hall, West Virginia University, Morgantown, WV 26506, USA
| | - Justin Legleiter
- The C. Eugene Bennett Department of Chemistry, 217 Clark Hall, West Virginia University, Morgantown, WV 26506, USA; Center for Neuroscience, Robert C. Byrd Health Sciences Center, PO Box 9304, West Virginia University, Morgantown, WV 26506, USA; NanoSAFE, PO Box 6223, West Virginia University, Morgantown, WV 26506, USA.
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40
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Qin SS, Yu YX, Li QK, Yu ZW. Interaction of Human Synovial Phospholipase A2 with Mixed Lipid Bilayers: A Coarse-Grain and All-Atom Molecular Dynamics Simulation Study. Biochemistry 2013; 52:1477-89. [DOI: 10.1021/bi3012687] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shan-Shan Qin
- Key Laboratory of Bioorganic
Phosphorous Chemistry and Chemical Biology (Ministry of Education),
Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Yang-Xin Yu
- Laboratory of Chemical Engineering
Thermodynamics, Department of Chemical Engineering, Tsinghua University, Beijing 100084, P. R. China
| | - Qi-Kai Li
- Department of Mechanical Engineering, Tsinghua University, Beijing 100084, P. R. China
| | - Zhi-Wu Yu
- Key Laboratory of Bioorganic
Phosphorous Chemistry and Chemical Biology (Ministry of Education),
Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
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41
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Jang H, Connelly L, Arce FT, Ramachandran S, Kagan BL, Lal R, Nussinov R. Mechanisms for the Insertion of Toxic, Fibril-like β-Amyloid Oligomers into the Membrane. J Chem Theory Comput 2013; 9:822-833. [PMID: 23316126 PMCID: PMC3539805 DOI: 10.1021/ct300916f] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Amyloid-β (Aβ) oligomers destabilize cellular ionic homeostasis, mediating Alzheimer's disease (AD). It is still unclear whether the mechanism (i) is mediated by cell surface receptors; (ii) is direct, with Aβ oligomers interacting with membrane lipids; or (iii) both mechanisms take place. Recent studies indicate that Aβ oligomers may act by either of the last two. Little is known about the oligomers' structures and how they spontaneously insert into the membrane. Using explicit solvent molecular dynamics (MD) simulations, we show that fibril-like Aβ(17-42) (p3) oligomer is capable of penetrating the membrane. Insertion is similar to that observed for protegrin-1 (PG-1), a cytolytic β-sheet-rich antimicrobial peptide (AMP). Both Aβ and PG-1 favor the amphipathic interface of the lipid bilayer in the early stage of interaction with the membrane. U-shaped Aβ oligomers are observed in solution and in the membrane, suggesting that the preformed seeds can be shared by amyloid fibrils in the growth phase and membrane toxicity. Here we provide sequential events in possible Aβ oligomer membrane-insertion pathways. We speculate that for the U-shaped motif, a trimer is the minimal oligomer size to insert effectively. We propose that monomers and dimers may insert in (apparently on-pathway) aggregation-intermediate β-hairpin state, and may (or may not) convert to a U-shape in the bilayer. Together with earlier observations, our results point to a non-specific, broadly heterogeneous landscape of membrane-inserting oligomer conformations, pathways, and membrane-mediated toxicity of β-rich oligomers.
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Affiliation(s)
- Hyunbum Jang
- Basic Science Program, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, USA
| | - Laura Connelly
- Departments of Bioengineering and of Mechanical and Aerospace Engineering, and Materials Science Program, University of California, San Diego, La Jolla, California 92093, USA
| | - Fernando Teran Arce
- Departments of Bioengineering and of Mechanical and Aerospace Engineering, and Materials Science Program, University of California, San Diego, La Jolla, California 92093, USA
| | - Srinivasan Ramachandran
- Departments of Bioengineering and of Mechanical and Aerospace Engineering, and Materials Science Program, University of California, San Diego, La Jolla, California 92093, USA
| | - Bruce L. Kagan
- Department of Psychiatry, David Geffen School of Medicine, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, California 90024, USA
| | - Ratnesh Lal
- Departments of Bioengineering and of Mechanical and Aerospace Engineering, and Materials Science Program, University of California, San Diego, La Jolla, California 92093, USA
| | - Ruth Nussinov
- Basic Science Program, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, USA
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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Robertson JWF, Kasianowicz JJ, Banerjee S. Analytical Approaches for Studying Transporters, Channels and Porins. Chem Rev 2012; 112:6227-49. [DOI: 10.1021/cr300317z] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Joseph W. F. Robertson
- Physical Measurement Laboratory,
National Institute of Standards and Technology, Gaithersburg, Maryland
20899, United States
| | - John J. Kasianowicz
- Physical Measurement Laboratory,
National Institute of Standards and Technology, Gaithersburg, Maryland
20899, United States
| | - Soojay Banerjee
- National
Institute of Neurological
Disorders and Stroke, Bethesda, Maryland 20824, United States
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Dalal V, Bhattacharya M, Narang D, Sharma PK, Mukhopadhyay S. Nanoscale Fluorescence Imaging of Single Amyloid Fibrils. J Phys Chem Lett 2012; 3:1783-1787. [PMID: 26291859 DOI: 10.1021/jz300687f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Amyloid formation is implicated in a variety of human diseases. It is important to perform high-resolution optical imaging of individual amyloid fibrils to delineate the structural basis of supramolecular protein assembly. However, amyloid fibrils do not lend themselves to the conventional microscopic resolution, which is hindered by the diffraction limit. Here we show super-resolution fluorescence imaging of fluorescently stained amyloid fibrils derived from disease-associated human β2-microglobulin using near-field scanning fluorescence microscopy. Using this technique, we were able to resolve the fibrils that were spatially separated by ∼75 nm. We have also been able to interrogate individual fibrils in a fibril-by-fibril manner by simultaneously monitoring both nanoscale topography and fluorescence brightness along the length of the fibrils. This method holds promise to detect conformational distributions and heterogeneity that are believed to correlate with the supramolecular packing of misfolded proteins within the fibrils in a diverse conformationally enciphered prion strains and amyloid polymorphs.
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Affiliation(s)
- Vijit Dalal
- †Department of Biological Sciences and ‡Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Mohali, Knowledge City, Sector 81, SAS Nagar, Mohali 140306, India
| | - Mily Bhattacharya
- †Department of Biological Sciences and ‡Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Mohali, Knowledge City, Sector 81, SAS Nagar, Mohali 140306, India
| | - Dominic Narang
- †Department of Biological Sciences and ‡Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Mohali, Knowledge City, Sector 81, SAS Nagar, Mohali 140306, India
| | - Pushpender K Sharma
- †Department of Biological Sciences and ‡Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Mohali, Knowledge City, Sector 81, SAS Nagar, Mohali 140306, India
| | - Samrat Mukhopadhyay
- †Department of Biological Sciences and ‡Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Mohali, Knowledge City, Sector 81, SAS Nagar, Mohali 140306, India
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